search for: probands

..., control = rpart.control(xval = 0)) for (i in 1:length(trees)) { trees[[i]] <- update(mod, weights = bootsamples[, i]) } } #bring in data [snip] #Recursive partitioning: library("rpart") # get a 2/3 random sample of ids ids <- sample(probands$id, size = 2*(length(probands$id))/3, replace = FALSE) # now I want a logical vector telling me which sample to put the # subjects in: #training_true <- probands$id %in% ids training <- subset(probands, probands$id %in% ids) testing <- subset(probands,...

Dear R listers, I have a data file looks like the following: Testing marker: s_1 --------------------------------------------- Allele df(0) -LnLk(0) df(T) -LnLk(T) ChiSq p 3 7995 29320.30 7994 29311.85 16.90 4e-05 (2229/8000 probands) Testing marker: s_2 --------------------------------------------- Allele df(0) -LnLk(0) df(T) -LnLk(T) ChiSq p 3 7995 29339.25 7994 29338.31 1.88 0.1702 ( 121/8000 probands) Testing marker: s_3 ------------------------------...

I am involved in a study where, as in most of life, men demonstrate themselves to be recalcitrant. So while we have many probands and most of their mothers we only have about 50% of the trios being complete. I have been running tdt and trio.types. It appears as if it is ignoring the duos. Sometimes a duo can be informative. For instance Father ..missing Mother 1/2 Proband 1/1 This duo shows that for allele 2, this was clearl...

Greetings all The help file for GAMM in mgcv indicates that the log likelihood for a GAMM reported using summary(my.gamm$lme) (as an example) is not correct. However, in a past R-help post (included below), there is some indication that the likelihood ratio test in anova.lme(mygamm$lme, mygamm1$lme) is valid. How can I tell if anova.lme results are meaningful (are AIC, BIC, and logLik

...function directly for loglikelihood and try to optimise using optim it gives warnings as well as error and if i use NLMINB then convergence is false. Can someone save my soul..... pl!!!!!!!!z below is my program script .............. #ovarian cancer data and parity among 769 probands and their mothers #cancer in proband y1<-c(1,1,1,1,1,1,1,rep(1,29),rep(1,36),rep(1,41),r! ep(1,85),rep(1,105),rep(1,84), 1,rep(0,22),rep(0,33),rep(0,38),rep(0,50),rep(0,103),rep(0,135)) #cancer in mother y2<-c(1,1,1,1,1,1,1,rep(0,29),rep(0,36),rep(0,41),rep(0,85),rep(0,...

Hello, i only got a small problem. i try to create automatic new dataframes, or png?s. the main problem i got is: how can i create automatic a new name for a file (read out by simply "for") - i tried to use "(paste...) but theres an errormessage, about a wrong declination. R told it is as.character, but need as.Real. Should i use another method than "paste"? i tried as

I am getting an error that I don't understand, and wonder if anyone could explain what's going on. I call a function defined thus: clogit.rds<-function(formula,data,extra.data,response.prob, na.action=getOption("na.action"),subset=NULL, control=coxph.control()){ method="exact" # only option for now mf<-match.call()

I tried to reproduce a result from a former colleague which he got with S-plus bootstrap method. I don't have S-plus at hand. In R, there are 2 packages related to bootstrap method, bootstrap and boot. The former has a function called 'bootstrap' but this does not seem to conform either to the function used in S-plus nor to that described in MASS, 3d ed., p.144. The latter seems to be

Bottom Line Up Front: How does one reshape genetic data from long to wide? I currently have a lot of data. About 180 individuals (some probands/patients, some parents, rare siblings) and SNP data from 6000 loci on each. The standard formats seem to be something along the lines of Famid, pid, fatid, motid, affected, sex, locus1Allele1, locus1Allele2, locus2Allele1, locus2Allele2, etc In other words one human, one row. If there were multipl...